1
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Spencer-Smith R, Morrison DK. Regulation of RAF family kinases: new insights from recent structural and biochemical studies. Biochem Soc Trans 2024; 52:1061-1069. [PMID: 38695730 DOI: 10.1042/bst20230552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 06/27/2024]
Abstract
The RAF kinases are required for signal transduction through the RAS-RAF-MEK-ERK pathway, and their activity is frequently up-regulated in human cancer and the RASopathy developmental syndromes. Due to their complex activation process, developing drugs that effectively target RAF function has been a challenging endeavor, highlighting the need for a more detailed understanding of RAF regulation. This review will focus on recent structural and biochemical studies that have provided 'snapshots' into the RAF regulatory cycle, revealing structures of the autoinhibited BRAF monomer, active BRAF and CRAF homodimers, as well as HSP90/CDC37 chaperone complexes containing CRAF or BRAFV600E. In addition, we will describe the insights obtained regarding how BRAF transitions between its regulatory states and examine the roles that various BRAF domains and 14-3-3 dimers play in both maintaining BRAF as an autoinhibited monomer and in facilitating its transition to an active dimer. We will also address the function of the HSP90/CDC37 chaperone complex in stabilizing the protein levels of CRAF and certain oncogenic BRAF mutants, and in serving as a platform for RAF dephosphorylation mediated by the PP5 protein phosphatase. Finally, we will discuss the regulatory differences observed between BRAF and CRAF and how these differences impact the function of BRAF and CRAF as drivers of human disease.
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Affiliation(s)
- Russell Spencer-Smith
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD 21702, U.S.A
| | - Deborah K Morrison
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD 21702, U.S.A
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2
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Ahmad M, Movileanu L. Multiplexed imaging for probing RAS-RAF interactions in living cells. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184173. [PMID: 37211322 PMCID: PMC10330472 DOI: 10.1016/j.bbamem.2023.184173] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 04/18/2023] [Accepted: 05/08/2023] [Indexed: 05/23/2023]
Abstract
GTP-bound RAS interacts with its protein effectors in response to extracellular stimuli, leading to chemical inputs for downstream pathways. Significant progress has been made in measuring these reversible protein-protein interactions (PPIs) in various cell-free environments. Yet, acquiring high sensitivity in heterogeneous solutions remains challenging. Here, using an intermolecular fluorescence resonance energy transfer (FRET) biosensing approach, we develop a method to visualize and localize HRAS-CRAF interactions in living cells. We demonstrate that the EGFR activation and the HRAS-CRAF complex formation can be concurrently probed in a single cell. This biosensing strategy discriminates EGF-stimulated HRAS-CRAF interactions at the cell and organelle membranes. In addition, we provide quantitative FRET measurements for assessing these transient PPIs in a cell-free environment. Finally, we prove the utility of this approach by showing that an EGFR-binding compound is a potent inhibitor of HRAS-CRAF interactions. The outcomes of this work form a fundamental basis for further explorations of the spatiotemporal dynamics of various signaling networks.
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Affiliation(s)
- Mohammad Ahmad
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA; Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, NY 13244, USA; The BioInspired Institute, Syracuse University, Syracuse, NY 13244, USA.
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3
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Liu C, Ye D, Yang H, Chen X, Su Z, Li X, Ding M, Liu Y. RAS-targeted cancer therapy: Advances in drugging specific mutations. MedComm (Beijing) 2023; 4:e285. [PMID: 37250144 PMCID: PMC10225044 DOI: 10.1002/mco2.285] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 04/06/2023] [Accepted: 04/18/2023] [Indexed: 05/31/2023] Open
Abstract
Rat sarcoma (RAS), as a frequently mutated oncogene, has been studied as an attractive target for treating RAS-driven cancers for over four decades. However, it is until the recent success of kirsten-RAS (KRAS)G12C inhibitor that RAS gets rid of the title "undruggable". It is worth noting that the therapeutic effect of KRASG12C inhibitors on different RAS allelic mutations or even different cancers with KRASG12C varies significantly. Thus, deep understanding of the characteristics of each allelic RAS mutation will be a prerequisite for developing new RAS inhibitors. In this review, the structural and biochemical features of different RAS mutations are summarized and compared. Besides, the pathological characteristics and treatment responses of different cancers carrying RAS mutations are listed based on clinical reports. In addition, the development of RAS inhibitors, either direct or indirect, that target the downstream components in RAS pathway is summarized as well. Hopefully, this review will broaden our knowledge on RAS-targeting strategies and trigger more intensive studies on exploiting new RAS allele-specific inhibitors.
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Affiliation(s)
- Cen Liu
- Beijing University of Chinese MedicineBeijingChina
| | - Danyang Ye
- Beijing University of Chinese MedicineBeijingChina
| | - Hongliu Yang
- Beijing University of Chinese MedicineBeijingChina
| | - Xu Chen
- Beijing University of Chinese MedicineBeijingChina
| | - Zhijun Su
- Beijing University of Chinese MedicineBeijingChina
| | - Xia Li
- Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Mei Ding
- Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Yonggang Liu
- Beijing University of Chinese MedicineBeijingChina
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4
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Okamoto K, Sako Y. Two Closed Conformations of CRAF Require the 14-3-3 Binding Motifs and Cysteine-Rich Domain to be Intact in Live Cells. J Mol Biol 2023; 435:167989. [PMID: 36736888 DOI: 10.1016/j.jmb.2023.167989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 02/04/2023]
Abstract
The protein rapidly accelerated fibrosarcoma (RAF) is a kinase downstream of the membrane protein RAS in the cellular signal transduction system. In the structure of RAF, the N- and C-terminus domains are connected with a flexible linker. The open/close dynamics and dimerization of RAF are thought to regulate its activity, although the details of these conformations are unknown, especially in live cells. In this work, we used alternating laser excitation to measure cytosolic CRAF in live HeLa cells and obtained single-molecule Förster resonance energy transfer (smFRET) distributions of the structural states. We compared the results for wild-type (WT)-CRAF before and after epidermal growth factor (EGF) stimulation, with mutations of the 14-3-3 binding sites and cysteine-rich domain, and an N-terminus truncation. The smFRET distributions of full-length CRAFs were analyzed by global fitting with three beta distributions. Our results suggested that a 14-3-3 dimer bound to two sites on a single CRAF molecule and induced the formation of the autoinhibitory closed conformation. There were two closed conformations, which the majority of WT-CRAF adopted. These two conformations showed different responsiveness to EGF stimulation.
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Affiliation(s)
- Kenji Okamoto
- Cellular Informatics Laboratory, Cluster for Pioneering Research, RIKEN, 2-1, Hirosawa, Wako, Saitama 351-0198, Japan.
| | - Yasushi Sako
- Cellular Informatics Laboratory, Cluster for Pioneering Research, RIKEN, 2-1, Hirosawa, Wako, Saitama 351-0198, Japan.
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5
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Qiao Y, Luo Y, Long N, Xing Y, Tu J. Single-Molecular Förster Resonance Energy Transfer Measurement on Structures and Interactions of Biomolecules. MICROMACHINES 2021; 12:492. [PMID: 33925350 PMCID: PMC8145425 DOI: 10.3390/mi12050492] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/21/2021] [Accepted: 04/23/2021] [Indexed: 12/15/2022]
Abstract
Single-molecule Förster resonance energy transfer (smFRET) inherits the strategy of measurement from the effective "spectroscopic ruler" FRET and can be utilized to observe molecular behaviors with relatively high throughput at nanometer scale. The simplicity in principle and configuration of smFRET make it easy to apply and couple with other technologies to comprehensively understand single-molecule dynamics in various application scenarios. Despite its widespread application, smFRET is continuously developing and novel studies based on the advanced platforms have been done. Here, we summarize some representative examples of smFRET research of recent years to exhibit the versatility and note typical strategies to further improve the performance of smFRET measurement on different biomolecules.
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Affiliation(s)
- Yi Qiao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China; (Y.Q.); (Y.L.); (N.L.)
| | - Yuhan Luo
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China; (Y.Q.); (Y.L.); (N.L.)
| | - Naiyun Long
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China; (Y.Q.); (Y.L.); (N.L.)
| | - Yi Xing
- Institute of Child and Adolescent Health, School of Public Health, Peking University, Beijing 100191, China;
| | - Jing Tu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China; (Y.Q.); (Y.L.); (N.L.)
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6
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Mclaurin JD, Weiner OD. Multiple sources of signal amplification within the B-cell Ras/MAPK pathway. Mol Biol Cell 2019; 30:1610-1620. [PMID: 31042097 PMCID: PMC6727637 DOI: 10.1091/mbc.e18-09-0560] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The Ras-Map kinase (MAPK) cascade underlies functional decisions in a wide range of cell types and organisms. In B-cells, positive feedback-driven Ras activation is the proposed source of the digital (all or none) MAPK responses following antigen stimulation. However, an inability to measure endogenous Ras activity in living cells has hampered our ability to test this model directly. Here we leverage biosensors of endogenous Ras and ERK activity to revisit this question. We find that B-cell receptor (BCR) ligation drives switch-like Ras activation and that lower BCR signaling output is required for the maintenance versus the initiation of Ras activation. Surprisingly, digital ERK responses persist in the absence of positive feedback-mediated Ras activation, and digital ERK is observed at a threshold level of Ras activation. These data suggest an independent analogue-to-digital switch downstream of Ras activation and reveal that multiple sources of signal amplification exist within the Ras-ERK module of the BCR pathway.
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Affiliation(s)
- Justin D Mclaurin
- Cardiovascular Research Institute and Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158
| | - Orion D Weiner
- Cardiovascular Research Institute and Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158
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7
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In-cell single-molecule FRET measurements reveal three conformational state changes in RAF protein. Biochim Biophys Acta Gen Subj 2019; 1864:129358. [PMID: 31071411 DOI: 10.1016/j.bbagen.2019.04.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 04/26/2019] [Accepted: 04/30/2019] [Indexed: 12/19/2022]
Abstract
BACKGROUND The structures of proteins are intimately related to their functions. Significant efforts have been dedicated to the structural investigation of proteins, mainly those of purified proteins in in vitro environments. Proteins function in living cells and thus protein structures must be regulated by interactions with various molecules, some of which participate in reaction networks, depending on the states, conditions, or actions of the cell. Therefore, it is very important to understand the structural behavior of proteins in living cells. METHODS Single-molecule Förster resonance energy transfer (smFRET) measurements were conducted using the alternative laser excitation (ALEX) technique. smFRET distributions of cytosolic Rapidly Accelerated Fibrosarcoma (RAF) proteins in living HeLa cells were obtained with exclusion of the negative effects of photobleached fluorophores and incompletely labeled proteins on smFRET. RESULTS smFRET histograms of wildtype (wt) RAF in live cells exhibited two major peaks, whereas that of the S621A mutant, which has been thought to have an expanded structure, was almost single-peaked. A population shift involving the peaks for wt RAF was detected upon epidermal growth factor stimulation. Spontaneous transitions between the conformational states corresponding to the two peaks were also detected using the FRET-two-channel kernel-based density distribution estimator method in comparison to static double-stranded DNA samples. CONCLUSIONS Cytosolic CRAF has at least three conformational states; in addition to the closed and open forms, the fully-open form was distinctly specified. Based on the results, we propose a speculative structural model for CRAF. GENERAL SIGNIFICANCE Structural distribution and changes to proteins in live cells as a result of intracellular interactions were successfully identified. smFRET using ALEX is applicable to any other cytosolic proteins.
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8
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Terrell EM, Morrison DK. Ras-Mediated Activation of the Raf Family Kinases. Cold Spring Harb Perspect Med 2019; 9:cshperspect.a033746. [PMID: 29358316 DOI: 10.1101/cshperspect.a033746] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The extracellular signal-regulated kinase (ERK) cascade comprised of the Raf, MEK, and ERK protein kinases constitutes a key effector cascade used by the Ras GTPases to relay signals regulating cell growth, survival, proliferation, and differentiation. Of the ERK cascade components, the regulation of the Raf kinases is by far the most complex, involving changes in subcellular localization, protein and lipid interactions, as well as alterations in the Raf phosphorylation state. The Raf kinases interact directly with active, membrane-localized Ras, and this interaction is often the first step in the Raf activation process, which ultimately results in ERK activation and the downstream phosphorylation of cellular targets that will specify a particular biological response. Here, we will examine our current understanding of how Ras promotes Raf activation, focusing on the molecular mechanisms that contribute to the Raf activation/inactivation cycle.
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Affiliation(s)
- Elizabeth M Terrell
- Laboratory of Cell and Developmental Signaling, NCI-Frederick, Frederick, Maryland 21702
| | - Deborah K Morrison
- Laboratory of Cell and Developmental Signaling, NCI-Frederick, Frederick, Maryland 21702
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9
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Yuan J, Ng WH, Lam PYP, Wang Y, Xia H, Yap J, Guan SP, Lee ASG, Wang M, Baccarini M, Hu J. The dimer-dependent catalytic activity of RAF family kinases is revealed through characterizing their oncogenic mutants. Oncogene 2018; 37:5719-5734. [PMID: 29930381 PMCID: PMC6202329 DOI: 10.1038/s41388-018-0365-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 05/18/2018] [Accepted: 05/21/2018] [Indexed: 12/19/2022]
Abstract
Although extensively studied for three decades, the molecular mechanisms that regulate the RAF/MEK/ERK kinase cascade remain ambiguous. Recent studies identified the dimerization of RAF as a key event in the activation of this cascade. Here, we show that in-frame deletions in the β3-αC loop activate ARAF as well as BRAF and other oncogenic kinases by enforcing homodimerization. By characterizing these RAF mutants, we find that ARAF has less allosteric and catalytic activity than the other two RAF isoforms, which arises from its non-canonical APE motif. Further, these RAF mutants exhibit a strong oncogenic potential, and a differential inhibitor resistance that correlates with their dimer affinity. Using these unique mutants, we demonstrate that active RAFs, including the BRAF(V600E) mutant, phosphorylate MEK in a dimer-dependent manner. This study characterizes a special category of oncogenic kinase mutations, and elucidates the molecular basis that underlies the differential ability of RAF isoforms to stimulate MEK-ERK pathway. Further, this study reveals a unique catalytic feature of RAF family kinases that can be exploited to control their activities for cancer therapies.
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Affiliation(s)
- Jimin Yuan
- Division of Cellular and Molecular Research, Singapore, Singapore
| | - Wan Hwa Ng
- Division of Cellular and Molecular Research, Singapore, Singapore
| | - Paula Y P Lam
- Division of Cellular and Molecular Research, Singapore, Singapore
- Cancer and Stem Cell Program, Duke-NUS Medical School, 8 College Road, 169857, Singapore, Singapore
| | - Yu Wang
- Division of Cellular and Molecular Research, Singapore, Singapore
| | - Hongping Xia
- Division of Cellular and Molecular Research, Singapore, Singapore
| | - Jiajun Yap
- Division of Cellular and Molecular Research, Singapore, Singapore
| | - Shou Ping Guan
- Division of Cellular and Molecular Research, Singapore, Singapore
| | - Ann S G Lee
- Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610, Singapore
- Office of Clinical & Academic Faculty Affairs, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
- Department of Physiology, National University of Singapore, 2 Medical Drive, 117597, Singapore, Singapore
| | - Mei Wang
- Cancer and Stem Cell Program, Duke-NUS Medical School, 8 College Road, 169857, Singapore, Singapore
| | - Manuela Baccarini
- Max F. Perutz Laboratories, University of Vienna, Doktor-Bohr-Gasse 9, 1030, Vienna, Austria
| | - Jiancheng Hu
- Division of Cellular and Molecular Research, Singapore, Singapore.
- Cancer and Stem Cell Program, Duke-NUS Medical School, 8 College Road, 169857, Singapore, Singapore.
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10
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Single-molecule fluorescence-based analysis of protein conformation, interaction, and oligomerization in cellular systems. Biophys Rev 2017; 10:317-326. [PMID: 29243093 PMCID: PMC5899725 DOI: 10.1007/s12551-017-0366-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 11/19/2017] [Indexed: 12/23/2022] Open
Abstract
Single-molecule imaging (SMI) of proteins in operation has a history of intensive investigations over 20 years and is now widely used in various fields of biology and biotechnology. We review the recent advances in SMI of fluorescently-tagged proteins in structural biology, focusing on technical applicability of SMI to the measurements in living cells. Basic technologies and recent applications of SMI in structural biology are introduced. Distinct from other methods in structural biology, SMI directly observes single molecules and single-molecule events one-by-one, thus, explicitly analyzing the distribution of protein structures and the history of protein dynamics. It also allows one to detect single events of protein interaction. One unique feature of SMI is that it is applicable in complicated and heterogeneous environments, including living cells. The numbers, location, movements, interaction, oligomerization, and conformation of single-protein molecules have been determined using SMI in cellular systems.
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11
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Nakamura Y, Umeki N, Abe M, Sako Y. Mutation-Specific Mechanisms of Hyperactivation of Noonan Syndrome SOS Molecules Detected with Single-molecule Imaging in Living Cells. Sci Rep 2017; 7:14153. [PMID: 29074966 PMCID: PMC5658395 DOI: 10.1038/s41598-017-14190-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 10/04/2017] [Indexed: 11/30/2022] Open
Abstract
Noonan syndrome (NS) is a congenital hereditary disorder associated with developmental and cardiac defects. Some patients with NS carry mutations in SOS, a guanine nucleotide exchange factor (GEF) for the small GTPase RAS. NS mutations have been identified not only in the GEF domain, but also in various domains of SOS, suggesting that multiple mechanisms disrupt SOS function. In this study, we examined three NS mutations in different domains of SOS to clarify the abnormality in its translocation to the plasma membrane, where SOS activates RAS. The association and dissociation kinetics between SOS tagged with a fluorescent protein and the living cell surface were observed in single molecules. All three mutants showed increased affinity for the plasma membrane, inducing excessive RAS signalling. However, the mechanisms by which their affinity was increased were specific to each mutant. Conformational disorder in the resting state, increased probability of a conformational change on the plasma membrane, and an increased association rate constant with the membrane receptor are the suggested mechanisms. These different properties cause the specific phenotypes of the mutants, which should be rescuable with different therapeutic strategies. Therefore, single-molecule kinetic analyses of living cells are useful for the pathological analysis of genetic diseases.
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Affiliation(s)
- Yuki Nakamura
- Cellular Informatics Laboratory, RIKEN, 2-1 Hirosawa, Wako, 351-0198, Japan
| | - Nobuhisa Umeki
- Cellular Informatics Laboratory, RIKEN, 2-1 Hirosawa, Wako, 351-0198, Japan
| | - Mitsuhiro Abe
- Cellular Informatics Laboratory, RIKEN, 2-1 Hirosawa, Wako, 351-0198, Japan
| | - Yasushi Sako
- Cellular Informatics Laboratory, RIKEN, 2-1 Hirosawa, Wako, 351-0198, Japan.
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12
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Li N, Zhao R, Sun Y, Ye Z, He K, Fang X. Single-molecule imaging and tracking of molecular dynamics in living cells. Natl Sci Rev 2017. [DOI: 10.1093/nsr/nww055] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Abstract
Unlike the ensemble-averaging measurements, the single-molecule imaging and tracking (SMIT) in living cells provides the real-time quantitative information about the locations, kinetics, dynamics and interactions of individual molecules in their native environments with high spatiotemporal resolution and minimal perturbation. The past decade has witnessed a transforming development in the methods of SMIT with living cells, including fluorescent probes, labeling strategies, fluorescence microscopy, and detection and tracking algorithms. In this review, we will discuss these aspects with a particular focus on their recent advancements. We will then describe representative single-molecule studies to illustrate how the single-molecule approaches can be applied to monitor biomolecular interaction/reaction dynamics, and extract the molecular mechanistic information for different cellular systems.
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Affiliation(s)
- Nan Li
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Molecular Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rong Zhao
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Molecular Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yahong Sun
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Molecular Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zi Ye
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Molecular Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kangmin He
- Department of Cell Biology, Harvard Medical School, and Cellular and Molecular Medicine Program, Boston Children's Hospital, Boston, MA 02115, USA
| | - Xiaohong Fang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Molecular Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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13
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Yoshizawa R, Umeki N, Yanagawa M, Murata M, Sako Y. Single-molecule fluorescence imaging of RalGDS on cell surfaces during signal transduction from Ras to Ral. Biophys Physicobiol 2017; 14:75-84. [PMID: 28744424 PMCID: PMC5515350 DOI: 10.2142/biophysico.14.0_75] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 04/29/2017] [Indexed: 01/28/2023] Open
Abstract
RalGDS is one of the Ras effectors and functions as a guanine nucleotide exchange factor for the small G-protein, Ral, which regulates membrane trafficking and cytoskeletal remodeling. The translocation of RalGDS from the cytoplasm to the plasma membrane is required for Ral activation. In this study, to understand the mechanism of Ras–Ral signaling we performed a single-molecule fluorescence analysis of RalGDS and its functional domains (RBD and REMCDC) on the plasma membranes of living HeLa cells. Increased molecular density of RalGDS and RBD, but not REMCDC, was observed on the plasma membrane after EGF stimulation of the cells to induce Ras activation, suggesting that the translocation of RalGDS involves an interaction between the GTP-bound active form of Ras and the RBD of RalGDS. Whereas the RBD played an important role in increasing the association rate constant between RalGDS and the plasma membrane, the REMCDC domain affected the dissociation rate constant from the membrane, which decreased after Ras activation or the hyperexpression of Ral. The Y64 residue of Ras and clusters of RalGDS molecules were involved in this reduction. From these findings, we infer that Ras activation not merely increases the cell-surface density of RalGDS, but actively stimulates the RalGDS–Ral interaction through a structural change in RalGDS and/or the accumulation of Ral, as well as the GTP–Ras/RalGDS clusters, to induce the full activation of Ral.
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Affiliation(s)
- Ryo Yoshizawa
- Cellular Informatics Lab., RIKEN, Wako, Saitama 351-0198, Japan.,Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan
| | - Nobuhisa Umeki
- Cellular Informatics Lab., RIKEN, Wako, Saitama 351-0198, Japan
| | | | - Masayuki Murata
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan
| | - Yasushi Sako
- Cellular Informatics Lab., RIKEN, Wako, Saitama 351-0198, Japan
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14
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van Haastert PJM, Keizer-Gunnink I, Kortholt A. Coupled excitable Ras and F-actin activation mediates spontaneous pseudopod formation and directed cell movement. Mol Biol Cell 2017; 28:922-934. [PMID: 28148648 PMCID: PMC5385941 DOI: 10.1091/mbc.e16-10-0733] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 12/19/2016] [Accepted: 01/26/2017] [Indexed: 11/29/2022] Open
Abstract
Chemotaxis is the mechanism by which cells move in the direction of chemical gradients. The central circuit connecting basal movement and gradient sensing is unknown. Ras activation and F-actin form one coupled excitable system, which is the beating heart of cell movement in both the absence and presence of external cues. Many eukaryotic cells regulate their mobility by external cues. Genetic studies have identified >100 components that participate in chemotaxis, which hinders the identification of the conceptual framework of how cells sense and respond to shallow chemical gradients. The activation of Ras occurs during basal locomotion and is an essential connector between receptor and cytoskeleton during chemotaxis. Using a sensitive assay for activated Ras, we show here that activation of Ras and F-actin forms two excitable systems that are coupled through mutual positive feedback and memory. This coupled excitable system leads to short-lived patches of activated Ras and associated F-actin that precede the extension of protrusions. In buffer, excitability starts frequently with Ras activation in the back/side of the cell or with F-actin in the front of the cell. In a shallow gradient of chemoattractant, local Ras activation triggers full excitation of Ras and subsequently F-actin at the side of the cell facing the chemoattractant, leading to directed pseudopod extension and chemotaxis. A computational model shows that the coupled excitable Ras/F-actin system forms the driving heart for the ordered-stochastic extension of pseudopods in buffer and for efficient directional extension of pseudopods in chemotactic gradients.
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Affiliation(s)
- Peter J M van Haastert
- Department of Cell Biochemistry, University of Groningen, 9747 AG Groningen, Netherlands
| | - Ineke Keizer-Gunnink
- Department of Cell Biochemistry, University of Groningen, 9747 AG Groningen, Netherlands
| | - Arjan Kortholt
- Department of Cell Biochemistry, University of Groningen, 9747 AG Groningen, Netherlands
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15
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Modeling Cellular Noise Underlying Heterogeneous Cell Responses in the Epidermal Growth Factor Signaling Pathway. PLoS Comput Biol 2016; 12:e1005222. [PMID: 27902699 PMCID: PMC5130170 DOI: 10.1371/journal.pcbi.1005222] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 10/25/2016] [Indexed: 12/03/2022] Open
Abstract
Cellular heterogeneity, which plays an essential role in biological phenomena, such as drug resistance and migration, is considered to arise from intrinsic (i.e., reaction kinetics) and extrinsic (i.e., protein variability) noise in the cell. However, the mechanistic effects of these types of noise to determine the heterogeneity of signal responses have not been elucidated. Here, we report that the output of epidermal growth factor (EGF) signaling activity is modulated by cellular noise, particularly by extrinsic noise of particular signaling components in the pathway. We developed a mathematical model of the EGF signaling pathway incorporating regulation between extracellular signal-regulated kinase (ERK) and nuclear pore complex (NPC), which is necessary for switch-like activation of the nuclear ERK response. As the threshold of switch-like behavior is more sensitive to perturbations than the graded response, the effect of biological noise is potentially critical for cell fate decision. Our simulation analysis indicated that extrinsic noise, but not intrinsic noise, contributes to cell-to-cell heterogeneity of nuclear ERK. In addition, we accurately estimated variations in abundance of the signal proteins between individual cells by direct comparison of experimental data with simulation results using Apparent Measurement Error (AME). AME was constant regardless of whether the protein levels varied in a correlated manner, while covariation among proteins influenced cell-to-cell heterogeneity of nuclear ERK, suppressing the variation. Simulations using the estimated protein abundances showed that each protein species has different effects on cell-to-cell variation in the nuclear ERK response. In particular, variability of EGF receptor, Ras, Raf, and MEK strongly influenced cellular heterogeneity, while others did not. Overall, our results indicated that cellular heterogeneity in response to EGF is strongly driven by extrinsic noise, and that such heterogeneity results from variability of particular protein species that function as sensitive nodes, which may contribute to the pathogenesis of human diseases. Individual cell behaviors are controlled by a variety of noise, such as fluctuations in biochemical reactions, protein variability, molecular diffusion, transcriptional noise, cell-to-cell contact, temperature, and pH. Such cellular noise often interferes with signal responses from external stimuli, and such heterogeneity functions in induction of drug resistance, survival, and migration of cells. Thus, heterogeneous cellular responses have positive and negative roles. However, the regulatory mechanisms that produce cellular heterogeneity are unclear. By mathematical modeling and simulations, we investigated how heterogeneous signaling responses are evoked in the EGF signaling pathway and influence the switch-like activation of nuclear ERK. This study demonstrated that cellular heterogeneity of the EGF signaling response is evoked by cell-to-cell variation of particular signaling proteins, such as EGFR, Ras, Raf, and MEK, which act as sensitive nodes in the pathway. These results suggest that signaling responses in individual cells can be predicted from the levels of proteins of sensitive nodes. This study also suggested that proteins of sensitive nodes may serve as cell survival mechanisms.
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16
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Zhou Y, Mao H, Joddar B, Umeki N, Sako Y, Wada KI, Nishioka C, Takahashi E, Wang Y, Ito Y. The significance of membrane fluidity of feeder cell-derived substrates for maintenance of iPS cell stemness. Sci Rep 2015; 5:11386. [PMID: 26065582 PMCID: PMC4464345 DOI: 10.1038/srep11386] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 04/22/2015] [Indexed: 11/09/2022] Open
Abstract
The biological activity of cell-derived substrates to maintain undifferentiated murine-induced pluripotent stem (iPS) cells was correlated to membrane fluidity as a new parameter of cell culture substrates. Murine embryonic fibroblasts (MEFs) were employed as feeder cells and their membrane fluidity was tuned by chemical fixation using formaldehyde (FA). Membrane fluidity was evaluated by real-time single-molecule observations of green fluorescent protein-labeled epidermal growth factor receptors on chemically fixed MEFs. Biological activity was monitored by colony formation of iPS cells. Treatment with a low concentration of FA sustained the membrane fluidity and biological activity, which were comparable to those of mitomycin C-treated MEFs. The biological activity was further confirmed by sustained expression of alkaline phosphatase, SSEA-1, and other pluripotency markers in iPS cells after 3-5 days of culture on FA-fixed MEFs. Chemical fixation of feeder cells has several advantages such as providing ready-to-use culture substrates without contamination by proliferating feeder cells. Therefore, our results provide an important basis for the development of chemically fixed culture substrates for pluripotent stem cell culture as an alternative to conventional treatment by mitomycin C or x-ray irradiation.
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Affiliation(s)
- Yue Zhou
- Nano Medical Engineering Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- School of Nursing, Nanjing University of Chinese Medicine, 138 Xianlin Road, Qixia District, Nanjing, Jiangsu Province 210023, China
- Department of Regenerative Medicine, School of Pharmaceutical Science, Jilin University, No.1266 Fujin Road, Changchun 130021, China
| | - Hongli Mao
- Nano Medical Engineering Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Binata Joddar
- Nano Medical Engineering Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Nobuhisa Umeki
- Cellular Informatics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yasushi Sako
- Cellular Informatics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Ken-Ichi Wada
- Nano Medical Engineering Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Chieko Nishioka
- Support Unit for Animal Experiment, Research Resources Center, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Eiki Takahashi
- Support Unit for Animal Experiment, Research Resources Center, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yi Wang
- Department of Regenerative Medicine, School of Pharmaceutical Science, Jilin University, No.1266 Fujin Road, Changchun 130021, China
| | - Yoshihiro Ito
- Nano Medical Engineering Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science, 2-1Hirosawa, Wako, Saitama 351-0198, Japan
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17
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Migliaccio N, Sanges C, Ruggiero I, Martucci NM, Rippa E, Arcari P, Lamberti A. Raf kinases in signal transduction and interaction with translation machinery. Biomol Concepts 2013; 4:391-9. [DOI: 10.1515/bmc-2013-0003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 03/17/2013] [Indexed: 12/12/2022] Open
Abstract
AbstractIn recent years, a large amount of evidence has given a central role to translational control in diseases such as cancer, tissue hypertrophy and neurodegeneration. Its deregulation can directly modulate cell cycling, transformation and survival response. The aim of this review is to describe the interaction between Raf activation and the main characters of the translational machinery, such as the elongation factor 1A (eEF1A), which has been recognized in recent years as one of the most interesting putative oncogenes. A particular emphasis is given to an intriguing non-canonical role that eEF1A can play in the relationship between the Ras→Raf-1→MEK1→ERK-1/2 and PI3K→Akt signaling pathways. Recently, our group has described a C-Raf kinase-mediated phosphorylation of eEF1A triggered by a survival pathway induced upon interferon alpha (IFNα) treatment in the human epidermoid cancer cell line (H1355). This phosphorylation seems to be the center of the survival pathway that counteracts the well-known pro-apoptotic function of IFNα. Furthermore, we have identified two new phosphorylation sites on eEF1A (Ser21 and Thr88) that are substrates for Raf kinases in vitro and, likely, in vivo as well. These residues seem to have a significant functional role in the control of cellular processes, such as cell proliferation and survival. In fact, overexpression of eEF1A2 in gemcitabine-treated cancer cells caused the upregulation of phosphoAkt and an increase in cell viability, thereby suggesting that eEF1A2 could exert its oncogenic behavior by participating in the regulation of PI3K pathway.
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Affiliation(s)
- Nunzia Migliaccio
- 1Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy
| | - Carmen Sanges
- 1Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy
| | - Immacolata Ruggiero
- 1Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy
| | - Nicola M. Martucci
- 1Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy
| | - Emilia Rippa
- 1Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy
| | | | - Annalisa Lamberti
- 1Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Naples, Italy
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18
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Affiliation(s)
- Tie Xia
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Key Laboratory of Molecular Nanostructures and Nanotechnology, Chinese Academy of Sciences, Beijing 100190, China;
| | - Nan Li
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Key Laboratory of Molecular Nanostructures and Nanotechnology, Chinese Academy of Sciences, Beijing 100190, China;
| | - Xiaohong Fang
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Key Laboratory of Molecular Nanostructures and Nanotechnology, Chinese Academy of Sciences, Beijing 100190, China;
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19
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Okamoto K, Sako Y. Variational Bayes analysis of a photon-based hidden Markov model for single-molecule FRET trajectories. Biophys J 2013; 103:1315-24. [PMID: 22995504 DOI: 10.1016/j.bpj.2012.07.047] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 07/27/2012] [Accepted: 07/30/2012] [Indexed: 11/29/2022] Open
Abstract
Single-molecule fluorescence resonance energy transfer (smFRET) measurement is a powerful technique for investigating dynamics of biomolecules, for which various efforts have been made to overcome significant stochastic noise. Time stamp (TS) measurement has been employed experimentally to enrich information within the signals, while data analyses such as the hidden Markov model (HMM) have been successfully applied to recover the trajectories of molecular state transitions from time-binned photon counting signals or images. In this article, we introduce the HMM for TS-FRET signals, employing the variational Bayes (VB) inference to solve the model, and demonstrate the application of VB-HMM-TS-FRET to simulated TS-FRET data. The same analysis using VB-HMM is conducted for other models and the previously reported change point detection scheme. The performance is compared to other analysis methods or data types and we show that our VB-HMM-TS-FRET analysis can achieve the best performance and results in the highest time resolution. Finally, an smFRET experiment was conducted to observe spontaneous branch migration of Holliday-junction DNA. VB-HMM-TS-FRET was successfully applied to reconstruct the state transition trajectory with the number of states consistent with the nucleotide sequence. The results suggest that a single migration process frequently involves rearrangement of multiple basepairs.
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Affiliation(s)
- Kenji Okamoto
- Advanced Science Institute, RIKEN, Wako, Saitama, Japan.
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20
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Dynamics of Ras complexes observed in living cells. SENSORS 2012; 12:9411-22. [PMID: 23012550 PMCID: PMC3444108 DOI: 10.3390/s120709411] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Revised: 06/29/2012] [Accepted: 07/04/2012] [Indexed: 11/17/2022]
Abstract
K-Ras works as a switch in many important intracellular signaling pathways and plays important roles in cell growth, proliferation, differentiation and carcinogenesis. For signal transduction from K-Ras to Raf1, the best-characterized effector of K-Ras, the general view is that Ras recruits Raf1 from the cytoplasm to the cell membrane. To elucidate this process, we constructed a series of fusion proteins (including Raf1 and K-Ras fused with either fluorescent proteins or fluorescent protein fragments) to compare subcellular localizations of these proteins. Bimolecular fluorescence complementation (BiFC) and a co-transfection system were used. In the BiFC system, the K-Ras/Raf1 complexes were mainly located in the cell membrane, while the Raf1 control was uniformly distributed in the cytoplasm. However, the complexes of Raf1 and K-RasC185S, a K-Ras mutant which loses membrane-localization, were also able to accumulate in the cell membrane. In contrast, an apparent cytosolic distribution pattern was observed in cells co-transfected with mcerulean-Raf1 and EGFP-K-RasC185S, suggesting that the membrane localization of K-Ras/Raf1 complexes is not entirely dependent on K-Ras, and that other factors, such as the irreversible conformation formed between K-Ras and Raf1 may play a role. This study sheds light on the interaction between K-Ras and Raf1 and provides a practical method to elucidate the mechanism underlying K-Ras and Raf1 binding to the cell membrane.
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21
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Suzuki KGN. Lipid rafts generate digital-like signal transduction in cell plasma membranes. Biotechnol J 2012; 7:753-61. [PMID: 22488962 DOI: 10.1002/biot.201100360] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Revised: 02/13/2012] [Accepted: 02/24/2012] [Indexed: 11/10/2022]
Abstract
Lipid rafts are meso-scale (5-200 nm) cell membrane domains where signaling molecules assemble and function. However, due to their dynamic nature, it has been difficult to unravel the mechanism of signal transduction in lipid rafts. Recent advanced imaging techniques have revealed that signaling molecules are frequently, but transiently, recruited to rafts with the aid of protein-protein, protein-lipid, and/or lipid-lipid interactions. Individual signaling molecules within the raft are activated only for a short period of time. Immobilization of signaling molecules by cytoskeletal actin filaments and scaffold proteins may facilitate more efficient signal transmission from rafts. In this review, current opinions of how the transient nature of molecular interactions in rafts generates digital-like signal transduction in cell membranes, and the benefits this phenomenon provides, are discussed.
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Affiliation(s)
- Kenichi G N Suzuki
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto, Japan.
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22
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23
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Sako Y, Hiroshima M, Pack CG, Okamoto K, Hibino K, Yamamoto A. Live cell single-molecule detection in systems biology. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2011; 4:183-92. [DOI: 10.1002/wsbm.161] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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24
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Hibino K, Shibata T, Yanagida T, Sako Y. Activation kinetics of RAF protein in the ternary complex of RAF, RAS-GTP, and kinase on the plasma membrane of living cells: single-molecule imaging analysis. J Biol Chem 2011; 286:36460-8. [PMID: 21862573 DOI: 10.1074/jbc.m111.262675] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
RAS is an important cell signaling molecule, regulating the activities of various effector proteins, including the kinase c-RAF (RAF). Despite the critical function of RAS signaling, the activation kinetics have not been analyzed experimentally in living cells for any of the RAS effectors. Here, we analyzed the kinetics of RAF activation on the plasma membrane in living HeLa cells after stimulation with EGF to activate RAS. RAF is recruited by the active form of RAS (RAS-GTP) from the cytoplasm to the plasma membrane through two RAS-binding sites (the RAS-binding domain and the cysteine-rich domain (CRD)) and is activated by its phosphorylation by still undetermined kinases on the plasma membrane. Using single-molecule imaging, we measured the dissociation time courses of GFP-tagged molecules of wild type RAF and fragments or mutants of RAF containing one or two of the three functional domains (the RAS-binding domain, the CRD, and the catalytic domain) to determine their interaction with membrane components. Each molecule showed a unique dissociation time course, indicating that both its interaction with RAS-GTP and its phosphorylation by the kinases are rate-limiting steps in RAF activation. Based on our experimental results, we propose a kinetic model for the activation of RAF. The model suggests the importance of the interaction between RAS-GTP and CRD for the effective activation of RAF, which is triggered by rapid RAS-GTP-induced conformational changes in RAF and the subsequent presentation of RAF to the kinase. The model also suggests necessary properties of the kinases that activate RAF.
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Affiliation(s)
- Kayo Hibino
- Cellular Informatics Laboratory, RIKEN, Advanced Science Institute, 2-1 Hirosawa, Wako 351-0198, Japan
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25
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Anderson DJ, Durieux JK, Song K, Alvarado R, Jackson PK, Hatzivassiliou G, Ludlam MJC. Live-cell microscopy reveals small molecule inhibitor effects on MAPK pathway dynamics. PLoS One 2011; 6:e22607. [PMID: 21829637 PMCID: PMC3150364 DOI: 10.1371/journal.pone.0022607] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Accepted: 06/26/2011] [Indexed: 12/19/2022] Open
Abstract
Oncogenic mutations in the mitogen activated protein kinase (MAPK) pathway are prevalent in human tumors, making this pathway a target of drug development efforts. Recently, ATP-competitive Raf inhibitors were shown to cause MAPK pathway activation via Raf kinase priming in wild-type BRaf cells and tumors, highlighting the need for a thorough understanding of signaling in the context of small molecule kinase inhibitors. Here, we present critical improvements in cell-line engineering and image analysis coupled with automated image acquisition that allow for the simultaneous identification of cellular localization of multiple MAPK pathway components (KRas, CRaf, Mek1 and Erk2). We use these assays in a systematic study of the effect of small molecule inhibitors across the MAPK cascade either as single agents or in combination. Both Raf inhibitor priming as well as the release from negative feedback induced by Mek and Erk inhibitors cause translocation of CRaf to the plasma membrane via mechanisms that are additive in pathway activation. Analysis of Erk activation and sub-cellular localization upon inhibitor treatments reveals differential inhibition and activation with the Raf inhibitors AZD628 and GDC0879 respectively. Since both single agent and combination studies of Raf and Mek inhibitors are currently in the clinic, our assays provide valuable insight into their effects on MAPK signaling in live cells.
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Affiliation(s)
- Daniel J. Anderson
- Department of Cell Regulation, Genentech, Inc., South San Francisco, California, United States of America
- * E-mail:
| | - Jenni K. Durieux
- Department of Cell Regulation, Genentech, Inc., South San Francisco, California, United States of America
| | - Kyung Song
- Department of Cancer Signaling, Genentech, Inc., South San Francisco, California, United States of America
| | - Ryan Alvarado
- Department of Cancer Signaling, Genentech, Inc., South San Francisco, California, United States of America
| | - Peter K. Jackson
- Department of Cell Regulation, Genentech, Inc., South San Francisco, California, United States of America
| | - Georgia Hatzivassiliou
- Department of Cancer Signaling, Genentech, Inc., South San Francisco, California, United States of America
| | - Mary J. C. Ludlam
- Department of Cell Regulation, Genentech, Inc., South San Francisco, California, United States of America
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26
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Udell CM, Rajakulendran T, Sicheri F, Therrien M. Mechanistic principles of RAF kinase signaling. Cell Mol Life Sci 2011; 68:553-65. [PMID: 20820846 PMCID: PMC11114552 DOI: 10.1007/s00018-010-0520-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Revised: 08/24/2010] [Accepted: 08/25/2010] [Indexed: 12/19/2022]
Abstract
The RAF family of kinases are key components acting downstream of receptor tyrosine kinases and cells employ several distinct mechanisms to strictly control their activity. RAF transitions from an inactive state, where the N-terminal regulatory region binds intramolecularly to the C-terminal kinase domain, to an open state capable of executing the phosphoryl transfer reaction. This transition involves changes both within and between the protein domains in RAF. Many different proteins regulate the transition between inactive and active states of RAF, including RAS and KSR, which are arguably the two most prominent regulators of RAF function. Recent developments have added several new twists to our understanding of RAF regulation. Among others, dimerization of the RAF kinase domain is emerging as a crucial step in the RAF activation process. The multitude of regulatory protein-protein interactions involving RAF remains a largely untapped area for therapeutic applications.
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Affiliation(s)
- Christian M. Udell
- Laboratory of Intracellular Signaling, Département de pathologie et de biologie cellulaire, Institute for Research in Immunology and Cancer, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montreal, QC H3C 3J7 Canada
| | - Thanashan Rajakulendran
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, Toronto, ON M5G 1X5 Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8 Canada
| | - Frank Sicheri
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, Toronto, ON M5G 1X5 Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8 Canada
| | - Marc Therrien
- Laboratory of Intracellular Signaling, Département de pathologie et de biologie cellulaire, Institute for Research in Immunology and Cancer, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montreal, QC H3C 3J7 Canada
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